Hello there,
I am using the VEP script (version 77) to analyse my variation data locally. It works fine on almost all chromosomes except chrY. For example, variant record "chrY 14107314" got annotation "ENSG00000235649" when using the website VEP, which is correct. However, when I use VEP locally, this record was assigned with "ENSG00000165246". The genome reference I am using is GRCh37.
My command is shown below : perl /home/software/ensembl-tools-release-77/scripts/variant_effect_predictor/variant_effect_predictor.pl -i input.vcf -o output.vep.vcf –offline –dir_cache /home/data/ensembl/cache –vcf –merged –force_overwrite –quiet –fork 10 –hgvs –assembly GRCh37 –everything
Can anyone give me some clue on this? Or telling me how I can track down the error? Thank you very much!
Best, Emma
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I see that you've posted an identical query to our Ensembl dev list. Please do not send the same issue to both Ensembl dev and BioStars as Ensembl provide support via both means, and posting to multiple locations can create duplicate work.